Figure 2.

Validation of ArchAlign. (a) The location of the TSSs was randomized by 50 to 250 bp for 200 structurally similar
TSSs from S. cerevisiae, and the nucleosome occupancy data, centered at the randomized TSS coordinates, were
aligned with ArchAlign. A total of 1.5 kb surrounding the TSSs is shown with -750
referring to the distance upstream and 750 referring to the distance downstream. (b) The TSS data were randomized by shifting the center upstream or downstream from the
actual location by a maximum distance of 50 to 250 bp at 25-bp intervals of increasing
randomization. The randomized TSS coordinates were then used to generate 1.5-kb regions
of nucleosome occupancy at 10-bp resolution surrounding the coordinates (blue line).
(c,e) Variability for the alignment of TSSs or origins was calculated as the average root
of sum of squares for that region compared to the mean profile. Variability for the
entire alignment was estimated as the average of all regions. The graphs show the
mean and standard error of each of the genomic features' ten alignments' overall variability
at each randomization. (d) The origins of replication were randomized as described above for TSSs and the randomized
coordinates were then used to generate 2-kb regions of nucleosome at 10-bp resolution
surrounding the coordinates (blue line). Randomized nucleosome occupancy regions were
then entered into ArchAlign using both the single-best-pair (red line) and seed sampling
(green line) approach. Each interval of randomization was repeated 10 times for a
total of 90 randomized datasets for each genomic feature. ArchAlign's output was then
tested for similarity to the original data by determining the percentage of aligned
TSSs and origins that were within 40 bp upstream or downstream of their original positions.